Description
SPRINGER Post Transcriptional Gene Regulation 3Ed (Hb 2022) by DASSI E.
This volume presents the most recent advances in techniques for studying the post-transcriptional regulation of gene expression (PTR). With sections on bioinformatics approaches, expression profiling, the protein and RNA interactome, the mRNA lifecycle, and RNA modifications, the book guides molecular biologists toward harnessing the power of this new generation of techniques, while also introducing the data analysis skills that these high-throughput techniques require. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Post-Transcriptional Gene Regulation, Third Edition serves as a versatile resource for researchers studying post-transcriptional regulation by both introducing the most recent techniques and providing a comprehensive guide to their implementation. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. Part I: Bioinformatics1. Introduction to Bioinformatics Resources for Post-Transcriptional Regulation of Gene ExpressionEliana Destefanis and Erik Dassi2. Predicting RNA Secondary Structure Using In Vitro and In Vivo DataRiccardo Delli Ponti and Gian Gaetano Tartaglia3. RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif EnvironmentInbal Paz, Amir Argoetti, Noa Cohen, Niv Even, and Yael Mandel-GutfreundPart II: Expression Studies4. Analysis of mRNA Translation by Polysome ProfilingAnne Cammas, Pauline Herviou, Leila Dumas, and Stefania Millevoi5. Exploring Ribosome-Positioning on Translating Transcripts with Ribosome ProfilingAlexander L. Cope, Sangeevan Vellappan, John S. Favate, Kyle S. Skalenko, Srujana S. Yadavalli, and Premal Shah6. Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-SeqSahil Sharma and Cynthia M. Sharma7. Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation SystemsKatharina G. Wandera and Chase L. BeiselPart III: Interactomics8. Studying RNP Composition with RIPAnnalisa Rossi and Alberto Inga9. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction SitesCharles Danan, Sudhir Manickavel, and Markus Hafner10. A Pipeline for Analyzing eCLIP and iCLIP Data with htseq-clip and DEWSeqSudeep Sahadevan, Thileepan Sekaran, and Thomas Schwarz11. Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH)Andrea Zeni, Margherita Grasso, and Michela A. Denti12. Identifying the Protein Interactomes of Target RNAs Using HyPR-MSKatherine B. Henke, Rachel M. Miller, Rachel A. Knoener, Mark Scalf, Michele Spiniello, and Lloyd M. SmithPart IV: The RNA Lifecycle13. Visualization and Quantification of Subcellular RNA Localization Using Single Molecule RNA Fluorescence In Situ HybridizationAnkita Arora, Raeann Goering, Pedro Tirado Velez, and J. Matthew Taliaferro14. Single-Molecule RNA Imaging Using Mango II ArraysAdam D. Cawte, Haruki Iino, Peter J. Unrau, and David S. Rueda15. Genome-Wide Identification of Polyadenylation Dynamics with TED-SeqYeonui Kwak and Hojoong Kwak16. In Vivo RNA Structure Probing with DMS-MaPseqParomita Gupta and Silvia Rouskin17. Transcriptome-Wide Profiling of RNA StabilityNina Fasching, Jan Petrzilek, Niko Popitsch, Veronika Herzog, and Stefan L. Ameres18. High-Throughput Quantitation of Yeast uORF Regulatory Impacts Using FACS-uORFGemma E. May and C. Joel McManusPart V: RNA Modifications19. m6A RNA Immunoprecipitation Followed by High-Throughput Sequencing to Map N6-MethyladenosineDevi Prasad Bhattarai and Francesca Aguilo20. Detecting m6A with In Vitro DART-SeqMatthew Tegowski1, Huanyu Zhu, and Kate D. Meyer21. Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon SequencingTennille Sibbritt, Ulrike Schumann, Andrew Shafik, Marco Guarnacci, Susan J. Clark, and Thomas Preiss22. Transcriptome-Wide Identification of 2'-O-Methylation Sites with RibOxi-SeqYinzhou Zhu, Christopher L. Holley, and Gordon G. Carmichael